Recent Developments in the Characterization of Nucleic Acid Hybridization Kinetics

Overview

Journal Curr Opin Biomed Eng

Specialty Biomedical Engineering

Date 2021 Aug 9

PMID 34368519

Citations 1

Authors

Yuan-I Chen

Manasa P Sripati

Trung Duc Nguyen

Yin-Jui Chang

Yu-An Kuo

Soonwoo Hong

Hsin-Chih Yeh

Affiliations

Soon will be listed here.

Abstract

Hybridization of nucleic acids (NAs) is a fundamental molecular mechanism that drives many cellular processes and enables new biotechnologies as well as therapeutics. However, existing methods that measure hybridization kinetics of nucleic acids are either performed at the ensemble level or constrained to non-native physiological conditions. Recent advances in 3D single-molecule tracking techniques break these limitations by allowing multiple annealing and melting events to be observed on a single oligonucleotide freely diffusing inside a live mammalian cell. This review provides an overview of diverse approaches to measuring NA hybridization kinetics at the single-molecule level and in live cells, and concludes with a synopsis of unresolved challenges and opportunities in the live-cell hybridization kinetics measurements. Important discoveries made by NA kinetics measurements and biotechnologies that can be improved with a deeper understanding of hybridization kinetics are also described.

Citing Articles

Recent Advances in Single-Molecule Tracking and Imaging Techniques.

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Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells.

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References

Michelini F, Jalihal A, Francia S, Meers C, Neeb Z, Rossiello F . From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev. 2018; 118(8):4365-4403. PMC: 7717669. DOI: 10.1021/acs.chemrev.7b00487. View

Hou S, Exell J, Welsher K . Real-time 3D single molecule tracking. Nat Commun. 2020; 11(1):3607. PMC: 7368020. DOI: 10.1038/s41467-020-17444-6. View

Gao Y, Wolf L, Georgiadis R . Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res. 2006; 34(11):3370-7. PMC: 1488884. DOI: 10.1093/nar/gkl422. View

Zhang J, Fang J, Duan W, Wu L, Zhang A, Dalchau N . Predicting DNA hybridization kinetics from sequence. Nat Chem. 2017; 10(1):91-98. PMC: 5739081. DOI: 10.1038/nchem.2877. View

Levi V, Ruan Q, Gratton E . 3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells. Biophys J. 2005; 88(4):2919-28. PMC: 1305386. DOI: 10.1529/biophysj.104.044230. View

Perillo E, Liu Y, Huynh K, Liu C, Chou C, Hung M . Deep and high-resolution three-dimensional tracking of single particles using nonlinear and multiplexed illumination. Nat Commun. 2015; 6:7874. PMC: 4532916. DOI: 10.1038/ncomms8874. View

Hayward S, Lund P, Kang Q, Johnson-Buck A, Tewari M, Walter N . Ultraspecific and Amplification-Free Quantification of Mutant DNA by Single-Molecule Kinetic Fingerprinting. J Am Chem Soc. 2018; 140(37):11755-11762. PMC: 6157911. DOI: 10.1021/jacs.8b06685. View

Peterson A, Heaton R, Georgiadis R . The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 2002; 29(24):5163-8. PMC: 97561. DOI: 10.1093/nar/29.24.5163. View

Roberts T, Langer R, Wood M . Advances in oligonucleotide drug delivery. Nat Rev Drug Discov. 2020; 19(10):673-694. PMC: 7419031. DOI: 10.1038/s41573-020-0075-7. View

10.

Bronson J, Fei J, Hofman J, Gonzalez Jr R, Wiggins C . Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys J. 2009; 97(12):3196-205. PMC: 2793368. DOI: 10.1016/j.bpj.2009.09.031. View

11.

Hadzic M, Borner R, Konig S, Kowerko D, Sigel R . Reliable State Identification and State Transition Detection in Fluorescence Intensity-Based Single-Molecule Förster Resonance Energy-Transfer Data. J Phys Chem B. 2018; 122(23):6134-6147. DOI: 10.1021/acs.jpcb.7b12483. View

12.

Liu C, Obliosca J, Liu Y, Chen Y, Jiang N, Yeh H . 3D single-molecule tracking enables direct hybridization kinetics measurement in solution. Nanoscale. 2017; 9(17):5664-5670. PMC: 5515391. DOI: 10.1039/c7nr01369h. View

13.

van de Meent J, Bronson J, Wiggins C, Gonzalez Jr R . Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments. Biophys J. 2014; 106(6):1327-37. PMC: 3985505. DOI: 10.1016/j.bpj.2013.12.055. View

14.

Kastantin M, Schwartz D . DNA hairpin stabilization on a hydrophobic surface. Small. 2012; 9(6):933-41. PMC: 3741999. DOI: 10.1002/smll.201202335. View

15.

Khvorova A, Watts J . The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 2017; 35(3):238-248. PMC: 5517098. DOI: 10.1038/nbt.3765. View

16.

Juette M, Bewersdorf J . Three-dimensional tracking of single fluorescent particles with submillisecond temporal resolution. Nano Lett. 2010; 10(11):4657-63. DOI: 10.1021/nl1028792. View

17.

Smith C, Zain R . Therapeutic Oligonucleotides: State of the Art. Annu Rev Pharmacol Toxicol. 2018; 59:605-630. DOI: 10.1146/annurev-pharmtox-010818-021050. View

18.

Chen Y, Chang Y, Nguyen T, Liu C, Phillion S, Kuo Y . Measuring DNA Hybridization Kinetics in Live Cells Using a Time-Resolved 3D Single-Molecule Tracking Method. J Am Chem Soc. 2019; 141(40):15747-15750. PMC: 7179573. DOI: 10.1021/jacs.9b08036. View

19.

Ha T, Tinnefeld P . Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu Rev Phys Chem. 2012; 63:595-617. PMC: 3736144. DOI: 10.1146/annurev-physchem-032210-103340. View

20.

Peterson E, Manhart M, Harris J . Single-Molecule Fluorescence Imaging of Interfacial DNA Hybridization Kinetics at Selective Capture Surfaces. Anal Chem. 2015; 88(2):1345-54. DOI: 10.1021/acs.analchem.5b03832. View